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FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: N97VQ

Calculation Name: 4GW4-H-Xray372

Preferred Name:

Target Type:

Ligand Name: 2-acetamido-2-deoxy-beta-d-glucopyranose

ligand 3-letter code: NAG

PDB ID: 4GW4

Chain ID: H

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-06-26

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptHSide
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 212
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2170728.92786
FMO2-HF: Nuclear repulsion 2089391.95835
FMO2-HF: Total energy -81336.96951
FMO2-MP2: Total energy -81575.940267


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy
"
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(H:1:PCA)


Summations of interaction energy for fragment #1(H:1:PCA)
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
-0.9481.4730.005-1.025-1.4010.002
Interaction energy analysis for fragmet #1(H:1:PCA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.014 / q_NPA : -0.016
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
frag_NumFragment number. ChainChain species. Res #Residue number. RES3-letter code of amino acid residue, ligand and solvent molecule. FCHARGEFormal charge [e]. q_MullikenFragment charge evaluated by Mulliken charge [e]. q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. DISTDistance from Ligand [Å]. TotalIFIE at MP2 level [kcal/mol]. ESElectro static interaction energy by PIEDA [kcal/mol]. EXExchange-repulsion energy by PIEDA [kcal/mol]. CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. DI(MP2)Dispersion energy by PIEDA [kcal/mol]. q(I=>J)Charge transfer value from I to J fragmens [e].
3H3HIS00.0260.0123.794-1.3070.577-0.006-0.841-1.0370.002
4H4LEU00.0060.0055.9120.6200.6200.0000.0000.0000.000
5H5SER0-0.0020.0059.6220.2370.2370.0000.0000.0000.000
6H6GLN00.024-0.01011.084-0.036-0.0360.0000.0000.0000.000
7H7SER00.0200.02414.7950.0710.0710.0000.0000.0000.000
8H8GLY00.0160.00617.740-0.024-0.0240.0000.0000.0000.000
9H9ALA0-0.050-0.02819.709-0.017-0.0170.0000.0000.0000.000
10H10ALA00.0290.02322.8830.0230.0230.0000.0000.0000.000
11H11VAL0-0.019-0.01225.828-0.005-0.0050.0000.0000.0000.000
12H12THR0-0.0030.00029.5320.0030.0030.0000.0000.0000.000
13H13LYS10.8930.94131.9260.0590.0590.0000.0000.0000.000
14H14PRO00.0290.00235.498-0.008-0.0080.0000.0000.0000.000
15H15GLY0-0.0010.00536.9950.0070.0070.0000.0000.0000.000
16H16ALA0-0.036-0.00634.3690.0000.0000.0000.0000.0000.000
17H17SER0-0.001-0.02831.534-0.011-0.0110.0000.0000.0000.000
18H18VAL0-0.0290.00126.1530.0120.0120.0000.0000.0000.000
19H19ARG10.8490.88723.2120.2050.2050.0000.0000.0000.000
20H20VAL0-0.043-0.00119.6040.0180.0180.0000.0000.0000.000
21H21SER00.028-0.00318.106-0.003-0.0030.0000.0000.0000.000
22H22CYS0-0.068-0.01514.082-0.043-0.0430.0000.0000.0000.000
23H23GLU-1-0.806-0.87511.125-0.333-0.3330.0000.0000.0000.000
24H24ALA0-0.035-0.0169.705-0.210-0.2100.0000.0000.0000.000
25H25SER00.0730.0275.9650.3080.3080.0000.0000.0000.000
26H26GLY00.0770.0353.652-1.654-1.4190.010-0.109-0.1360.000
27H27TYR0-0.054-0.0444.068-0.1400.1620.001-0.075-0.2280.000
28H28LYS10.9450.9716.7901.5561.5560.0000.0000.0000.000
29H29ILE00.0600.0239.2540.0840.0840.0000.0000.0000.000
30H30SER0-0.018-0.01512.0650.0830.0830.0000.0000.0000.000
31H31ASP-1-0.932-0.97913.750-0.671-0.6710.0000.0000.0000.000
32H32HIS0-0.0070.02611.764-0.118-0.1180.0000.0000.0000.000
33H33PHE00.0080.00514.999-0.008-0.0080.0000.0000.0000.000
34H34ILE00.0180.02312.986-0.107-0.1070.0000.0000.0000.000
35H35HIS0-0.002-0.01516.7660.1420.1420.0000.0000.0000.000
36H36TRP0-0.013-0.00917.818-0.064-0.0640.0000.0000.0000.000
37H37TRP00.001-0.00718.6540.0790.0790.0000.0000.0000.000
38H38ARG10.8330.89421.5190.2450.2450.0000.0000.0000.000
39H39GLN0-0.023-0.01522.572-0.019-0.0190.0000.0000.0000.000
40H40ALA00.0460.03824.9990.0120.0120.0000.0000.0000.000
41H41PRO00.004-0.00827.966-0.009-0.0090.0000.0000.0000.000
42H42GLY00.0160.01328.5340.0110.0110.0000.0000.0000.000
43H43GLN0-0.034-0.01828.3190.0070.0070.0000.0000.0000.000
44H44GLY00.0400.03026.603-0.015-0.0150.0000.0000.0000.000
45H45LEU0-0.0020.00120.3750.0070.0070.0000.0000.0000.000
46H46GLN0-0.008-0.01224.6590.0250.0250.0000.0000.0000.000
47H47TRP0-0.016-0.00422.5170.0170.0170.0000.0000.0000.000
48H48VAL0-0.029-0.01223.8680.0360.0360.0000.0000.0000.000
49H49GLY00.047-0.00723.6260.0380.0380.0000.0000.0000.000
50H50TRP0-0.0320.02121.340-0.043-0.0430.0000.0000.0000.000
51H51ILE0-0.010-0.01819.2530.0540.0540.0000.0000.0000.000
52H52ASN00.0260.02519.664-0.094-0.0940.0000.0000.0000.000
53H53PRO00.0530.02516.1790.0690.0690.0000.0000.0000.000
54H54LYS10.9330.98117.7200.6240.6240.0000.0000.0000.000
55H55THR0-0.011-0.01120.4370.0310.0310.0000.0000.0000.000
56H56GLY0-0.0060.01222.5220.0330.0330.0000.0000.0000.000
57H57GLN0-0.010-0.00523.6840.0030.0030.0000.0000.0000.000
58H58PRO00.0120.00724.484-0.038-0.0380.0000.0000.0000.000
59H59ASN0-0.015-0.01825.8090.0460.0460.0000.0000.0000.000
60H60ASN0-0.026-0.01726.268-0.018-0.0180.0000.0000.0000.000
61H61ALA00.0380.02328.2400.0160.0160.0000.0000.0000.000
62H62ARG10.9960.98330.1660.1990.1990.0000.0000.0000.000
63H63GLN00.0000.01632.1020.0010.0010.0000.0000.0000.000
64H64PHE0-0.037-0.02728.4790.0120.0120.0000.0000.0000.000
65H65GLN00.0630.04232.188-0.002-0.0020.0000.0000.0000.000
66H66GLY00.0230.01833.6480.0130.0130.0000.0000.0000.000
67H67ARG10.6950.80232.6090.1870.1870.0000.0000.0000.000
68H68VAL00.0360.02227.0510.0020.0020.0000.0000.0000.000
69H69SER0-0.052-0.00827.4500.0020.0020.0000.0000.0000.000
70H70LEU0-0.0080.01022.800-0.006-0.0060.0000.0000.0000.000
71H71THR0-0.005-0.00722.9560.0120.0120.0000.0000.0000.000
72H72ARG10.8890.92118.2960.3720.3720.0000.0000.0000.000
73H73GLN0-0.047-0.01818.6290.0530.0530.0000.0000.0000.000
74H74ALA00.0020.01116.120-0.043-0.0430.0000.0000.0000.000
75H74SER00.017-0.00513.5140.0370.0370.0000.0000.0000.000
76H74TRP0-0.021-0.02615.905-0.039-0.0390.0000.0000.0000.000
77H74ASP-1-0.822-0.89113.448-0.168-0.1680.0000.0000.0000.000
78H75PHE0-0.086-0.04313.961-0.061-0.0610.0000.0000.0000.000
79H76ASP-1-0.895-0.9388.123-0.824-0.8240.0000.0000.0000.000
80H77THR0-0.059-0.0438.698-0.350-0.3500.0000.0000.0000.000
81H78TYR0-0.060-0.02410.8170.1780.1780.0000.0000.0000.000
82H78SER0-0.018-0.01513.142-0.077-0.0770.0000.0000.0000.000
83H79PHE0-0.044-0.03713.6000.0340.0340.0000.0000.0000.000
84H80TYR0-0.002-0.01317.8880.0160.0160.0000.0000.0000.000
85H81MET00.0000.00721.133-0.014-0.0140.0000.0000.0000.000
86H82ASP-1-0.789-0.86623.550-0.200-0.2000.0000.0000.0000.000
87H83LEU0-0.023-0.01027.046-0.003-0.0030.0000.0000.0000.000
88H84LYS10.9710.99529.4680.1630.1630.0000.0000.0000.000
89H85ALA0-0.005-0.00733.133-0.005-0.0050.0000.0000.0000.000
90H86VAL0-0.054-0.00431.204-0.004-0.0040.0000.0000.0000.000
91H87ARG10.9010.92434.2460.1610.1610.0000.0000.0000.000
92H88SER00.0600.01334.363-0.001-0.0010.0000.0000.0000.000
93H89ASP-1-0.832-0.92633.778-0.151-0.1510.0000.0000.0000.000
94H90ASP-1-0.783-0.83330.314-0.195-0.1950.0000.0000.0000.000
95H91THR00.0270.03229.068-0.008-0.0080.0000.0000.0000.000
96H92ALA0-0.021-0.01225.978-0.001-0.0010.0000.0000.0000.000
97H93ILE00.0120.02320.3220.0090.0090.0000.0000.0000.000
98H94TYR0-0.015-0.02021.519-0.014-0.0140.0000.0000.0000.000
99H95PHE00.0330.01416.4130.0010.0010.0000.0000.0000.000
100H97ALA00.0250.00913.451-0.089-0.0890.0000.0000.0000.000
101H98ARG10.8760.9268.4212.2102.2100.0000.0000.0000.000
102H99GLN0-0.041-0.01313.1340.0330.0330.0000.0000.0000.000
103H100ARG10.7860.88711.6301.0621.0620.0000.0000.0000.000
104H101SER00.007-0.02414.4170.0380.0380.0000.0000.0000.000
105H102ASP-1-0.874-0.94317.784-0.553-0.5530.0000.0000.0000.000
106H103PHE0-0.053-0.03720.6750.0410.0410.0000.0000.0000.000
107H104TRP0-0.054-0.02619.5610.0180.0180.0000.0000.0000.000
108H105ASP-1-0.732-0.82116.204-0.823-0.8230.0000.0000.0000.000
109H106PHE00.022-0.00814.761-0.070-0.0700.0000.0000.0000.000
110H107ASP-1-0.796-0.87610.419-1.750-1.7500.0000.0000.0000.000
111H108VAL00.0000.0076.999-0.174-0.1740.0000.0000.0000.000
112H109TRP0-0.013-0.0169.8540.2350.2350.0000.0000.0000.000
113H110GLY00.0380.02010.598-0.177-0.1770.0000.0000.0000.000
114H111SER0-0.018-0.02012.4370.0610.0610.0000.0000.0000.000
115H112GLY0-0.0120.00213.9230.0810.0810.0000.0000.0000.000
116H113THR0-0.062-0.03117.4370.0210.0210.0000.0000.0000.000
117H114GLN00.0050.00019.927-0.016-0.0160.0000.0000.0000.000
118H115VAL00.0240.01723.3900.0200.0200.0000.0000.0000.000
119H116THR00.0190.00426.2390.0010.0010.0000.0000.0000.000
120H117VAL0-0.016-0.00629.5990.0110.0110.0000.0000.0000.000
121H118SER0-0.026-0.01832.7050.0060.0060.0000.0000.0000.000
122H119SER00.0610.00335.6100.0000.0000.0000.0000.0000.000
123H120ALA00.0040.03537.3900.0060.0060.0000.0000.0000.000
124H121SER00.0430.00836.437-0.004-0.0040.0000.0000.0000.000
125H122THR0-0.046-0.02633.726-0.002-0.0020.0000.0000.0000.000
126H123LYS10.8830.93535.8100.0150.0150.0000.0000.0000.000
127H124GLY00.0390.03436.671-0.002-0.0020.0000.0000.0000.000
128H125PRO0-0.014-0.01136.051-0.004-0.0040.0000.0000.0000.000
129H126SER0-0.034-0.01338.6560.0050.0050.0000.0000.0000.000
130H127VAL00.0160.01439.156-0.004-0.0040.0000.0000.0000.000
131H128PHE00.0020.00041.8700.0040.0040.0000.0000.0000.000
132H129PRO00.0530.03743.581-0.001-0.0010.0000.0000.0000.000
133H130LEU0-0.039-0.01042.165-0.003-0.0030.0000.0000.0000.000
134H131ALA00.0380.01445.7990.0020.0020.0000.0000.0000.000
135H132PRO0-0.0100.00147.820-0.003-0.0030.0000.0000.0000.000
136H141THR0-0.042-0.02345.2710.0010.0010.0000.0000.0000.000
137H142ALA0-0.040-0.02447.078-0.002-0.0020.0000.0000.0000.000
138H143ALA00.0140.00444.1400.0000.0000.0000.0000.0000.000
139H144LEU0-0.0060.01742.4910.0010.0010.0000.0000.0000.000
140H145GLY00.052-0.00241.090-0.002-0.0020.0000.0000.0000.000
141H146CYS0-0.035-0.02039.7220.0030.0030.0000.0000.0000.000
142H147LEU0-0.0110.00139.632-0.004-0.0040.0000.0000.0000.000
143H148VAL0-0.033-0.01335.7920.0040.0040.0000.0000.0000.000
144H149LYS10.9060.91238.0740.0260.0260.0000.0000.0000.000
145H150ASP-1-0.785-0.86639.587-0.028-0.0280.0000.0000.0000.000
146H151TYR00.0290.02332.2570.0090.0090.0000.0000.0000.000
147H152PHE0-0.0070.02533.404-0.008-0.0080.0000.0000.0000.000
148H153PRO00.041-0.00529.9010.0110.0110.0000.0000.0000.000
149H154GLU-1-0.869-0.92128.282-0.076-0.0760.0000.0000.0000.000
150H155PRO0-0.018-0.01025.316-0.001-0.0010.0000.0000.0000.000
151H156VAL0-0.012-0.02828.3820.0110.0110.0000.0000.0000.000
152H157THR0-0.043-0.01127.165-0.001-0.0010.0000.0000.0000.000
153H158VAL00.020-0.00630.0040.0040.0040.0000.0000.0000.000
154H159SER0-0.029-0.00131.7440.0030.0030.0000.0000.0000.000
155H160TRP00.0680.02633.566-0.003-0.0030.0000.0000.0000.000
156H161ASN00.0100.00136.5410.0010.0010.0000.0000.0000.000
157H162SER00.0110.00134.3850.0070.0070.0000.0000.0000.000
158H163GLY0-0.035-0.01232.2420.0100.0100.0000.0000.0000.000
159H164ALA0-0.0180.00033.0320.0020.0020.0000.0000.0000.000
160H165LEU0-0.032-0.01235.895-0.003-0.0030.0000.0000.0000.000
161H166THR00.004-0.01031.099-0.004-0.0040.0000.0000.0000.000
162H167SER00.0130.00433.677-0.009-0.0090.0000.0000.0000.000
163H168GLY00.0500.01935.4580.0010.0010.0000.0000.0000.000
164H169VAL0-0.059-0.02933.961-0.004-0.0040.0000.0000.0000.000
165H170HIS00.0110.01133.747-0.007-0.0070.0000.0000.0000.000
166H171THR0-0.031-0.02031.4040.0060.0060.0000.0000.0000.000
167H172PHE0-0.024-0.01731.853-0.007-0.0070.0000.0000.0000.000
168H173PRO00.0200.00629.9950.0050.0050.0000.0000.0000.000
169H174ALA0-0.033-0.01131.1950.0050.0050.0000.0000.0000.000
170H175VAL00.0240.02132.947-0.011-0.0110.0000.0000.0000.000
171H176LEU0-0.023-0.01434.6510.0070.0070.0000.0000.0000.000
172H177GLN0-0.066-0.04836.7270.0030.0030.0000.0000.0000.000
173H178SER00.0400.01040.348-0.002-0.0020.0000.0000.0000.000
174H179SER0-0.0030.00141.810-0.001-0.0010.0000.0000.0000.000
175H180GLY00.0330.02138.7800.0000.0000.0000.0000.0000.000
176H181LEU0-0.079-0.03437.1670.0000.0000.0000.0000.0000.000
177H182TYR00.0400.02332.158-0.005-0.0050.0000.0000.0000.000
178H183SER0-0.008-0.00736.2100.0110.0110.0000.0000.0000.000
179H184LEU00.0080.02232.357-0.007-0.0070.0000.0000.0000.000
180H185SER00.002-0.02136.1370.0060.0060.0000.0000.0000.000
181H186SER00.0090.02835.280-0.005-0.0050.0000.0000.0000.000
182H187VAL00.0280.00136.8200.0040.0040.0000.0000.0000.000
183H188VAL00.0220.01937.5940.0000.0000.0000.0000.0000.000
184H189THR0-0.032-0.01139.650-0.001-0.0010.0000.0000.0000.000
185H190VAL00.0180.01141.8180.0040.0040.0000.0000.0000.000
186H191PRO00.0500.03444.483-0.004-0.0040.0000.0000.0000.000
187H192SER00.043-0.01047.6720.0020.0020.0000.0000.0000.000
188H193SER00.0130.01450.7130.0000.0000.0000.0000.0000.000
189H194SER0-0.018-0.00447.1680.0020.0020.0000.0000.0000.000
190H195LEU00.0240.01247.8020.0030.0030.0000.0000.0000.000
191H196GLY00.0240.02350.0200.0010.0010.0000.0000.0000.000
192H197THR0-0.046-0.02649.3900.0010.0010.0000.0000.0000.000
193H198GLN0-0.0160.01244.3980.0050.0050.0000.0000.0000.000
194H199THR00.0110.00644.279-0.003-0.0030.0000.0000.0000.000
195H200TYR0-0.003-0.01442.0000.0040.0040.0000.0000.0000.000
196H201ILE0-0.031-0.03640.926-0.003-0.0030.0000.0000.0000.000
197H202CYM-1-0.802-0.86238.5570.0190.0190.0000.0000.0000.000
198H203ASN00.0090.00235.6990.0060.0060.0000.0000.0000.000
199H204VAL00.0360.01634.5560.0000.0000.0000.0000.0000.000
200H205ASN0-0.030-0.01731.1170.0100.0100.0000.0000.0000.000
201H206HIS10.8240.88331.496-0.006-0.0060.0000.0000.0000.000
202H207LYS11.0150.98824.707-0.110-0.1100.0000.0000.0000.000
203H208PRO00.0260.03128.5560.0060.0060.0000.0000.0000.000
204H209SER00.0190.01530.675-0.004-0.0040.0000.0000.0000.000
205H210ASN0-0.059-0.02833.0970.0050.0050.0000.0000.0000.000
206H211THR00.0100.01334.503-0.002-0.0020.0000.0000.0000.000
207H212LYS10.9660.95731.518-0.093-0.0930.0000.0000.0000.000
208H213VAL00.0060.03036.6280.0020.0020.0000.0000.0000.000
209H214ASP-1-0.919-0.96238.4470.0470.0470.0000.0000.0000.000
210H215LYS10.8830.93540.708-0.014-0.0140.0000.0000.0000.000
211H216ARG10.9830.99343.004-0.039-0.0390.0000.0000.0000.000
212H217VAL0-0.0180.00443.406-0.004-0.0040.0000.0000.0000.000